Over the past two decades, an appreciation that nascent RNA polymerase II (Pol II) transcripts participate in numerous enzymatic reactions has emerged. For example, Beyer and co-workers have directly visualized nascent pre-mRNA shortening owing to intron removal by the spliceosome (Beyer and Osheim, 1988; Osheim et al., 1985). Such an event is considered to be `co-transcriptional', because it occurs before RNA synthesis is complete and while the nascent RNA is still tethered to the DNA by the polymerase (Fig. 1). Observations of contemporaneous synthesis and processing raise possibilities for co-regulation among chemical reactions, and this has been intensely investigated in recent years. The term co-transcriptional has come to imply a functionally significant coupling between transcription and RNA processing events. However, some reactions may occur during transcription, simply because they are relatively fast compared with the time it takes to transcribe the gene to its end. Here, I focus on the relationships between pre-mRNA synthesis and processing in order to address the following question: when is it important to be co-transcriptional?
Fig. 1. Co-transcriptional pre-mRNA processing. A schematic representation of transcription and pre-mRNA processing events at Pol II transcription units (TUs). Pol II (black ball) initiates transcription at the promoter (arrow) and proceeds along the TU during elongation phase, terminating and releasing from the DNA template following passage through the polyadenylation signals. Several polyadenylation factors, such as CPSF and CstF, bind directly to Pol II and are shown all along the TU as a blue ball adjacent to the black one. Capping enzymes (red oval) bind to Pol II as it enters the elongation phase and then fall off the TU. The 5' cap added by the capping enzymes is symbolized by the baseball cap. Because splicing is co-transcriptional, we have hypothetically placed splicing factors recognizing the 5' and 3' splice sites (orange and yellow balls, respectively) and the assembly of the spliceosome (green oval) within the body of the TU. Additional polyadenylation factors are recruited to downstream regions, as shown by the additional dark blue ball. At termination, Pol II is released from the template and recycled, and the fragment of cleaved nascent RNA remaining will be degraded. The mRNP is released from the template and undergoes nuclear transport.
What goes on at transcription units (TUs)? From the point of view of Pol II, the transcription process includes pre-initiation complex formation, transcription initiation, elongation, termination and dissociation of Pol II from the DNA template (Fig. 1). From the point of view of the transcript, pre-mRNA processing includes five processes: (1) 5' end capping, in which the 5' triphosphate of the pre-mRNA is cleaved and a guanosine monophosphate is added and subsequently methylated to produce m7GpppN; (2) editing, in which individual RNA residues are converted to alternative bases (e.g. adenosine is converted to inosine by base deamination) to produce mRNAs encoding distinct protein products; (3) splicing, in which introns are removed and exons are ligated together by the spliceosome; (4) 3' end formation, which involves pre-mRNA cleavage and synthesis of the poly(A) tail; and paradoxically (5) degradation. A priori, each of these modifications might occur independently of the others, since most can occur in in vitro reconstituted systems on purified pre-mRNA substrates. However, many studies have revealed functional relationships between these processes and each (with the exception of editing) has been shown to be co-transcriptional at least some of the time. Importantly, a number of trans-acting factors required for pre-mRNA processing directly bind to Pol II, which stimulates processing, and, in some cases, processing feeds back to Pol II activity. This has led to the proposal that transcription and processing occur in a `gene expression factory' composed of machines linked together for the purposes of efficiency and regulation (Bentley, 2002; Cook, 1999; Maniatis and Reed, 2002; Proudfoot et al., 2002).